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[MRG] allow copyfile_brainvision to work with .dat extension #1008

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merged 3 commits into from
May 16, 2022
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[MRG] allow copyfile_brainvision to work with .dat extension #1008

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a1623d2
allow copyfile_brainvision to work with .dat extension
dominikwelke May 16, 2022
1efecfa
pep style
dominikwelke May 16, 2022
fa6e0dd
add to changelog
dominikwelke May 16, 2022
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3 changes: 3 additions & 0 deletions doc/whats_new.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ The following authors had contributed before. Thank you for sticking around!
* `Richard Höchenberger`_
* `Robert Luke`_
* `Stefan Appelhoff`_
* `Dominik Welke`_

Detailed list of changes
~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -63,6 +64,8 @@ Detailed list of changes

- The MNE-BIDS Inspector didn't work if ``mne-qt-browser`` was installed and used as the default plotting backend, as the Inspector currently only supports the Matplotlib backend, by `Richard Höchenberger`_ (:gh:`1007`)

- :func:`mne.copyfiles.copyfile_brainvision` can now deal with ``.dat`` file extension, by `Dominik Welke`_ (:gh:`1008`)

:doc:`Find out what was new in previous releases <whats_new_previous_releases>`

.. include:: authors.rst
30 changes: 17 additions & 13 deletions mne_bids/copyfiles.py
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Expand Up @@ -73,7 +73,7 @@ def _get_brainvision_encoding(vhdr_file):


def _get_brainvision_paths(vhdr_path):
"""Get the .eeg and .vmrk file paths from a BrainVision header file.
"""Get the .eeg/.dat and .vmrk file paths from a BrainVision header file.

Parameters
----------
Expand All @@ -83,7 +83,7 @@ def _get_brainvision_paths(vhdr_path):
Returns
-------
paths : tuple
Paths to the .eeg file at index 0 and the .vmrk file at index 1 of
Paths to the .eeg/.dat file at index 0 and the .vmrk file at index 1 of
the returned tuple.

"""
Expand All @@ -100,10 +100,11 @@ def _get_brainvision_paths(vhdr_path):
with open(vhdr_path, 'r', encoding=enc) as f:
lines = f.readlines()

# Try to find data file .eeg
eeg_file_match = re.search(r'DataFile=(.*\.eeg)', ' '.join(lines))
# Try to find data file .eeg/.dat
eeg_file_match = re.search(r'DataFile=(.*\.(eeg|dat))', ' '.join(lines))

if not eeg_file_match:
raise ValueError('Could not find a .eeg file link in'
raise ValueError('Could not find a .eeg or .dat file link in'
f' {vhdr_path}')
else:
eeg_file = eeg_file_match.groups()[0]
Expand Down Expand Up @@ -154,7 +155,7 @@ def copyfile_ctf(src, dest):
"""
_copytree(src, dest)
# list of file types to rename
file_types = ('.acq', '.eeg', '.hc', '.hist', '.infods', '.bak',
file_types = ('.acq', '.eeg', '.dat', '.hc', '.hist', '.infods', '.bak',
'.meg4', '.newds', '.res4')
# Rename files in dest with the name of the dest directory
fnames = [f for f in os.listdir(dest) if f.endswith(file_types)]
Expand Down Expand Up @@ -266,10 +267,11 @@ def _anonymize_brainvision(vhdr_file, date):
def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=None):
"""Copy a BrainVision file triplet to a new location and repair links.

The BrainVision file format consists of three files: .vhdr, .eeg, and .vmrk
The .eeg and .vmrk files associated with the .vhdr file will be given names
as in `vhdr_dest` with adjusted extensions. Internal file pointers will be
fixed.
The BrainVision file format consists of three files:
.vhdr, .eeg/.dat, and .vmrk
The .eeg/.dat and .vmrk files associated with the .vhdr file will be
given names as in `vhdr_dest` with adjusted extensions. Internal file
pointers will be fixed.

Parameters
----------
Expand Down Expand Up @@ -319,17 +321,19 @@ def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=None):
# extract encoding from brainvision header file, or default to utf-8
enc = _get_brainvision_encoding(vhdr_src)

# Copy data .eeg ... no links to repair
# Copy data .eeg/.dat ... no links to repair
sh.copyfile(eeg_file_path, fname_dest + '.eeg')

# Write new header and marker files, fixing the file pointer links
# For that, we need to replace an old "basename" with a new one
# assuming that all .eeg, .vhdr, .vmrk share one basename
# assuming that all .eeg/.dat, .vhdr, .vmrk share one basename
__, basename_src = op.split(fname_src)
assert basename_src + '.eeg' == op.split(eeg_file_path)[-1]
assert op.split(eeg_file_path)[-1] in [
basename_src + '.eeg', basename_src + '.dat']
assert basename_src + '.vmrk' == op.split(vmrk_file_path)[-1]
__, basename_dest = op.split(fname_dest)
search_lines = ['DataFile=' + basename_src + '.eeg',
'DataFile=' + basename_src + '.dat',
'MarkerFile=' + basename_src + '.vmrk']

with open(vhdr_src, 'r', encoding=enc) as fin:
Expand Down